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That's an interesting point.
I had forgotten this but I have also changed the cage plates as I thought they had got slightly bent when the mech got ripped off and old hanger snapped (when I had them off they didn't actually seem bent). So its kind of a new mech that has never worked properly. It's possible I didn't put the new plates on right, or the mech got bent somewhere else than the cage.
It could be good to borrow one of your mechs if you have a spare to see if that works. I expect it would but good to check.
Also Hanger alignment. I was ruling this out on the basis that I've put two new hangers on with the same result but the (carbon) frame could have got slightly bent at the dropout when the mech was ripped off.
I'll look into crash mode first then come back to you, as that will be easiest and I would like to understand it better.If it is either bent mech or the hanger alignment it still shifts perfectly over 10 / 11 gears. Did audax on Saturday with no shift issues all day. Makes me think it is more likely to be software, but not impossible.
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Generally I've found with bent stuff you get odd shifting in a couple of cogs changes. But it's possible you bent it evenly enough (or messed up the cage swap in some way - wrong part? missed a washer?) that has evenly pushed the whole cage too far in one direction.
I've got to go to the dentist today, over your way. The Mason is currently in bits so I could bring you the RD off it (but I'll need it back soon). It's probably not perfect (I dropped it a couple of times) but it definitely shifts into all cogs on my bike so would be a good test.
Are you around today? Depends how the dentist visit goes but I could come over later or this eve and have a proper go at it.
Do you want to borrow my hanger straightener tool just to make sure the hanger is aligned? If you bent a hanger though, you could also have bent the derailler itself so what I'd do is test the hanger alignment is ok, if it is, swap in another RD and see if that works across the whole range (I've got a couple of Ultegra ones you could use). If that works and the borked RD with the limit screws wound out doesn't work then it's probably a bent RD.